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Cobalt in PDB 2gru: Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase Complexed with Carbaglucose-6-Phosphate, Nad+ and CO2+

Protein crystallography data

The structure of Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase Complexed with Carbaglucose-6-Phosphate, Nad+ and CO2+, PDB code: 2gru was solved by E.Nango, T.Kumasaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.72 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.569, 70.108, 81.569, 90.00, 117.61, 90.00
R / Rfree (%) 17.4 / 22.3

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase Complexed with Carbaglucose-6-Phosphate, Nad+ and CO2+ (pdb code 2gru). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase Complexed with Carbaglucose-6-Phosphate, Nad+ and CO2+, PDB code: 2gru:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 2gru

Go back to Cobalt Binding Sites List in 2gru
Cobalt binding site 1 out of 2 in the Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase Complexed with Carbaglucose-6-Phosphate, Nad+ and CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase Complexed with Carbaglucose-6-Phosphate, Nad+ and CO2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co601

b:14.4
occ:1.00
OE1 A:GLU183 2.0 11.0 1.0
OBI A:EXO607 2.1 20.4 1.0
NE2 A:HIS262 2.1 13.8 1.0
NE2 A:HIS246 2.2 16.2 1.0
OBG A:EXO607 2.3 29.4 1.0
O A:HOH695 2.3 24.4 1.0
CD2 A:HIS262 2.9 15.1 1.0
CBB A:EXO607 3.0 29.7 1.0
CD A:GLU183 3.0 10.6 1.0
CBA A:EXO607 3.0 30.6 1.0
CE1 A:HIS246 3.1 16.7 1.0
CD2 A:HIS246 3.2 17.3 1.0
CE1 A:HIS262 3.3 14.6 1.0
OE2 A:GLU183 3.4 7.8 1.0
OD2 A:ASP135 3.9 19.5 1.0
CG A:HIS262 4.2 15.4 1.0
ND1 A:HIS246 4.2 16.9 1.0
ND1 A:HIS262 4.3 15.9 1.0
CG A:GLU183 4.3 11.5 1.0
CG A:HIS246 4.3 17.7 1.0
CG1 A:ILE266 4.4 15.7 1.0
O A:HOH728 4.4 20.6 1.0
CBC A:EXO607 4.4 31.1 1.0
CBF A:EXO607 4.4 35.4 1.0
NZ A:LYS186 4.5 10.8 1.0
O A:HOH754 4.8 38.7 1.0
CD1 A:ILE266 4.8 13.3 1.0
OBJ A:EXO607 4.8 33.1 1.0
CBH A:EXO607 4.9 38.2 1.0

Cobalt binding site 2 out of 2 in 2gru

Go back to Cobalt Binding Sites List in 2gru
Cobalt binding site 2 out of 2 in the Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase Complexed with Carbaglucose-6-Phosphate, Nad+ and CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase Complexed with Carbaglucose-6-Phosphate, Nad+ and CO2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co602

b:14.4
occ:1.00
OE1 B:GLU183 2.0 12.9 1.0
NE2 B:HIS262 2.1 9.9 1.0
OAH B:CAK609 2.1 21.3 1.0
NE2 B:HIS246 2.2 14.0 1.0
OAG B:CAK609 2.3 19.5 1.0
O B:HOH701 2.6 24.8 1.0
CD2 B:HIS262 2.9 11.6 1.0
CD B:GLU183 3.0 11.3 1.0
CE1 B:HIS246 3.0 17.4 1.0
CAB B:CAK609 3.1 28.2 1.0
CE1 B:HIS262 3.1 12.4 1.0
CAA B:CAK609 3.1 29.3 1.0
CD2 B:HIS246 3.3 13.6 1.0
OE2 B:GLU183 3.4 9.8 1.0
OD2 B:ASP135 3.9 13.3 1.0
O B:HOH635 4.1 33.3 1.0
CG B:HIS262 4.1 14.5 1.0
ND1 B:HIS262 4.2 16.5 1.0
ND1 B:HIS246 4.2 13.0 1.0
CG B:GLU183 4.2 9.9 1.0
CG1 B:ILE266 4.3 19.2 1.0
CG B:HIS246 4.3 13.7 1.0
CAC B:CAK609 4.4 30.0 1.0
O B:HOH745 4.5 43.3 1.0
CAF B:CAK609 4.5 33.7 1.0
NZ B:LYS186 4.6 10.9 1.0
CD1 B:ILE266 4.7 17.1 1.0
OAI B:CAK609 4.9 32.3 1.0

Reference:

E.Nango, T.Kumasaka, T.Hirayama, N.Tanaka, T.Eguchi. Structure of 2-Deoxy-Scyllo-Inosose Synthase, A Key Enzyme in the Biosynthesis of 2-Deoxystreptamine-Containing Aminoglycoside Antibiotics, in Complex with A Mechanism-Based Inhibitor and Nad+ Proteins V. 70 517 2008.
ISSN: ISSN 0887-3585
PubMed: 17879343
DOI: 10.1002/PROT.21526
Page generated: Tue Jul 30 15:14:43 2024

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